The Yorkshire club had previously admitted a charge of using an unlicensed agent when they signed Anthony Elding from Stockport County in January 2008.
The striker has since moved on to Crewe Alexandra following a six-month spell at Elland Road.
Leeds have also been warned as to their future conduct with the fine of £12,500 suspended until September 1, 2010.
However, the punishment is significantly less severe that the £25,000 fines handed down to Crystal Palace and an agent last month over the transfer of Nick Carle to Selhurst Park from Bristol City.